Improved staining boxes for fast, uniform staining of ultrathin sections on grids.

A standard LKB (LKB-Produkter Ab. S-161, 25 Brommma 1, Sweden) grid storage box is converted into several grid staining boxes by sawing the body of the box into segments along rows of its grid storage cavities. The staining boxes can be cut out to any required size or shape. The polymethyacrylate storage box cover is discarded. Covers for the staining boxes are cut from thin sheet vinyl, which is more chemically resistant than polymethyacrylate. Corresponding 2 mm diameter holes are drilled through the vinyl covers and the bottoms of the grid storage cavities of the staining boxes to convert the storage cavities into staining chambers. For staining, the covers are tied to the boxes with sewing thread and the assembled units are put into vials. The separate staining chambers prevent intermingling of and mechanical damage to grids during the staining procedure. Ultrathin sections are more cleanly and uniformly stained in bulk by the use of these staining boxes than they are when stained individually by a standard method.     

Improved Staining Boxes for Fast, Uniform Staining of Ultrathin Sections on Grids

A standard LKB (LKB-Produkter Ab. S161, 45 Bromma 1, Sweden) grid storage box is converted into several grid staining boxes by sawing the body of the box into segments along rows of its grid storage cavities. the staining boxes can be cut out to any required size or shape. the polymethacrylate storage box cover is discarded. Covers for the staining boxes are cut from thin sheet vinyl, which is more chemically resistant thin polymethacrylate. Corresponding 2 mm diameter holes are drilled through the vinyl covers and the bottoms of the grid storage cavities of the staining boxes to convert the storage cavities into staining chambers. for staining, the covers are tied to the boxes with sewing thread and the assembled units are put into vials. the separate staining chambers prevent intermingling of and mechanical damage to grids during the staining procedure. Ultrathin sections are more cleanly and uniformly stained in bulk by the use of these staining boxes than they are when stained individually by a standard method.     

Specific nest box designs can improve habitat restoration for cavity‐dependent arboreal mammals

Tree‐cavity‐dependent wildlife faces future shortages of cavities due to a decline in the abundance of large, old trees in many parts of the world. Nest boxes are proposed as a tool to restore habitat value but evidence of their effectiveness for arboreal mammals remains equivocal. This may arise from a poor understanding of design preferences. We conducted investigations in two landscapes in eastern Australia to determine whether species show a preference for specific designs. We observed a preference by some mammal species for particular designs (33–78% occupied/used), suggesting that design refinement can improve the frequency with which nest boxes are used. Although feral species may out‐compete target species for nest boxes, we did not observe this. We recorded feral honeybees (Apis mellifera) in 6–9% of nest boxes but they did not remain, and many occupied boxes were later used by mammals. The introduced common myna bird (Acridotheres tristis) was prevalent in one landscape, but competition for nest boxes was localized. For nest boxes to be an effective habitat restoration tool, they must be able to be occupied over long periods of time. We investigated this for the squirrel glider (Petaurus norfolcensis), an arboreal marsupial threatened through part of its geographic range. Squirrel gliders occupied and bred within nest boxes (100% used) at two locations continuously over a 10‐year period with minimal nest box maintenance. Individuals occupied boxes for up to 7 years. This confirms that targeted nest box programs can be an effective restoration tool for cavity‐dependent arboreal mammals.     

Outcomes of decades long installation of nest boxes for arboreal mammals in southern Australia

Nest boxes are commonly installed to support hollow‐using species where the abundance of hollow‐bearing trees is deficient. Recent studies have provided equivocal evidence about the effectiveness of nest box projects and have highlighted significant management costs associated with some projects. We document the functionality of 303 nest boxes installed across five different community‐led projects in southern Australia for periods of 10–25 years. As expected, we found that nest boxes lost functionality over time. However, 60% remained functional to support the Brush‐tailed Phascogale (Phascogale tapoatafa) and the Sugar Glider (Petaurus breviceps) after almost 20 years. Years installed, method of nest box attachment and tree species influenced whether boxes remained functional. Nest box construction material changed over time so could not be assessed specifically. When inspected in a single year, the Brush‐tailed Phascogale occupied 9% of functional boxes and another 48% contained their nests. The Sugar Glider occupied 15% of functional boxes and another 22% contained their nests. These values suggest the nest box installations were highly effective for these species, although more detailed study is needed to understand what contribution these installations have made to support the local populations. Maintenance of most nest boxes occurred twice a year in the first five years after installation, but many received no maintenance for periods of three years, and some 10–15 years, before our census. Our findings suggest that infrequent maintenance by community groups can sustain nest box projects over periods of several decades. Research into employing nest boxes as a management tool in Australia is still in its infancy. Further studies are needed to resolve factors that limit their effectiveness.     

A moorable,automated plankton sampler

A moorable, automated plankton sampler is described, designed to obtain series of plankton samples over extended time periods in the absence of a surface vessel. The sampler consists of one or more net-containing boxes, a unit for generating as well as measuring water flow through the net boxes, a programmeable control unit, and a frame. Each net box contains several nets on a vinyl strip, used to move the nets from the storage chamber into the fishing position and then into the preservative chamber. Preservation of samples is in a formalin-brine mixture.Net boxes can be added and the number of nets per box changed; the prototype is described with 1 net box with 10 nets. Volume of water to be filtered, time between sample collections, number of net boxes and the number of nets in each box is programmed into the control unit before sampler deployment. Collections made with the sampler are compared with those made with a SCOR net and a pump.     

The influence of the simulation box geometry in solid-state molecular simulations: phase behaviour of lithium iodide in a dynamic Monte Carlo simulation

In thermodynamic computer simulations, it is common to use cubic simulation boxes, which are then regarded as unit cells of an infinitely large cubic lattice. While this approach is adequate for gases and liquids at low densities, for dense liquids and solid cuboid boxes forming an orthorhombic lattice or parallelepiped boxes forming a triclinic lattice are shown to be advantageous, because they do not predetermine the structure of the simulated system. In this work, an extension of the Ewald summation formalism towards a parallelepiped lattice symmetry is given. Monte Carlo simulations of lithium iodide with cubic, cuboid and parallelepiped box geometries are reported; the latter is found to offer little improvement over the cuboid geometry. The existence of two hexagonal solid phases is discussed.     

Architecture of the Streptomyces lividans DnaA protein-replication origin complexes

The Streptomyces oriC region contains two clusters of 19 DnaA boxes separated by a spacer (134 bp). The Streptomyces DnaA protein consists, like all other DnaA proteins, of four domains: domain III and the carboxyterminal part (domain IV) are responsible for binding of ATP and DNA, respectively. Binding of the DnaA protein to the entire oriC region analysed by electron microscopy showed that the DnaA protein forms separate complexes at each of the clusters of DnaA boxes, but not at the spacer separating them. In vivo mutational analysis revealed that the number of DnaA boxes and the presence of the spacer linking both groups of DnaA boxes seem to be important for a functional Streptomyces origin. We suggest that the arrangement of DnaA boxes allows the DNA-bound DnaA protein to induce bending and looping of the oriC region. As it was shown by electrophoretic mobility shift assay and "one hybrid system", two domains, I and III, facilitate interactions between DnaA molecules. We postulate that domain I and domain III could be involved in cooperativity at distant and at closely spaced DnaA boxes, respectively. The long domain II extends the range over which N termini (domain I) of DNA-bound DnaA protein can form dimers. Thus, interactions between DnaA molecules may bring two clusters of DnaA boxes separated by the spacer into functional contact by loop formation. Removal of the spacer region or deletion of domains I and II resulted, respectively, in nucleoprotein complexes which are not fully developed, or huge nucleoprotein aggregates.     

Selection of nest sites by a hole-nesting duck, the Goldeneye Bucephala clangula

Nest site preferences were examined for a population of Goldeneye Ducks breeding in nest boxes in Värmland, central Sweden. Some nest boxes were occupied more often than others even if females returning to the same nest box were excluded from the analysis. Nest boxes located higher up trees were occupied more often than those close to the ground and some spatial 'cluster groups' of boxes were occupied more often than others. Otherwise nest site prefernces were not related to any measured physical attributes of the boxes. Prefernces for nest boxes seemed to be based mainly on a tendency for females to select those that had been occupied by other females in the preceding year, especially if they had bred successfully. As a result of this, the occupancy of nest boxes was not random over years but rather progressed in a series of runs; a period of consecutive years in which a box was occupied was followed by a period of years in which it was empty.
There were reproductive consequences for these prefernces in that females occupying preferred boxes were less likely to lose their clutch to a predator. These females also bred earlier in the year and produced larger clutches and broods than females breeding in other boxes.     

Hierarchy and positive/negative interplays of the hepatocyte nuclear factors HNF-1, -3 and -4 in the liver-specific enhancer for the human alpha-1-microglobulin/bikunin precursor.

Alpha-1-microglobulin and bikunin are two plasma glycoproteins encoded by an alpha-1-microglobulin/bikunin precursor (AMBP) gene. The strict liver-specific expression of the AMBP gene is controlled by a potent enhancer made of six clustered boxes numbered 1-6 that have been reported to be proven or potential binding sites for the hepatocyte-enriched nuclear factors HNF-1, -4, -3, -1, -3, -4, respectively. In the present study, electromobility shift assays of wild-type or mutated probes demonstrated that the boxes 1-5 have a binding capacity for their cognate HNF protein. Box 5 is also a target for another, as yet unidentified, factor. A functional analysis of the wild-type or mutated enhancer, driving its homologous promoter and a reporter CAT gene in the HepG2 hepatoma cell line, demonstrated that all six boxes participate in the enhancer activity, with the primary influence of box 4 (HNF-1) and box 2 (HNF-4). A similar analysis in the HNF-free CHO cell line co-transfected with one or several HNF factors further demonstrated various interplays between boxes: box 3 (HNF-3 alpha and beta) has a negative influence over the major HNF-4 box 2 as well as a positive influence over the major HNF-1 box 4.     

The value of 'bat boxes' for attracting hollow-dependent fauna to farm forestry plantations in southeast Queensland

Summary Small artificial nest/roost boxes, originally designed for microbats, were deployed in three farm forest plantations and at one native forest site in southeast Queensland in order to assess their use by vertebrates and their contribution toward enhancing biodiversity in plantation forests through the provision of habitat. Two sites were located in a relatively 'intact' forest landscape (SF 351 and Strano) and two sites in a more 'fragmented' or 'variegated' landscape (Askham and Thomas). Twenty-four boxes were placed at each site over an area covering approximately 1.2–1.8 ha. Each site was checked from five (SF 351) to nine (Askham) times between April 1996 and November 2000. The artificial nest/roost boxes were attractive to a range of small fauna that included Feathertail Gliders ( Acrobates pygmaeus ), Sugar Gliders ( Petaurus breviceps ), Squirrel Gliders ( Petaurus norfolcensis ) and the Yellow-footed Marsupial Mouse ( Antechinus flavipes ), all of which constructed nests inside boxes. Gould's Long-eared Bats ( Nyctophilus gouldi ) used boxes primarily as roosts and maternity sites. In general, fewer animals were recorded in boxes at the two sites located within a relatively 'intact' landscape, while the highest numbers of animals were recorded in boxes in two farm forest plantations within 'variegated' landscapes. The availability of alternative natural hollows and landscape factors appear to be important determinants of the extent to which boxes are occupied. The present study indicates that the biodiversity of farm forests can be enhanced through simple habitat manipulation utilizing artificial roosting or nesting boxes.
Key words Antechinus, biodiversity, farm forestry, glider, marsupial, microbat, nest box, roost.     

Efficacy of intervention to relieve nest box competition for Orange‐bellied Parrot Neophema chrysogaster

We use an experimental approach to evaluate the effectiveness of removing nests of a dominant competitor to create vacant nest boxes for a critically endangered parrot. We compared the number of times that Tree Martin (Petrochelidon nigricans – the dominant competitor at nest boxes) perched at or entered nest boxes intended for Orange‐bellied Parrot (Neophema chrysogaster – the subordinate nest competitor) over three time periods (before, immediately after and one week after experimental nest destruction). In the before period, rates of nest attendance by martins in treatment and control nests were not explained by treatment group. After experimental nest destruction, total attendance at boxes by martins rose to a mean of 6.1 visits over three five‐minute surveys in the treatment group, compared with 3.3 visits at control boxes. Within individual surveys, martins visited treatment boxes 4.4 times per survey one week after nest destruction, compared with only 1.6 visits in the control group. Martins in the treatment group rapidly rebuilt their nests and laid replacement clutches, and within a week, all boxes were reoccupied. Nest destruction did not increase nesting opportunities for the parrot, and increased vigilance of the dominant competitor may in fact reduce nesting opportunities in nearby boxes. Our study suggests that removing martin nests is an ineffective management action for alleviating nest competition for this parrot.     

Life cycle assessment of single use thermoform boxes made from polystyrene (PS), polylactic acid, (PLA), and PLA/starch: cradle to consumer gate

Purpose

Currently, the bio-based plastics have been drawing considerable attention from the packaging industry as a sustainable solution for replacing petroleum-based plastics in order to reduce the accumulation of plastic waste in the environment. This work has benchmarked the environmental impact of bio-based against petroleum-based plastics for single use boxes. In this paper, the cradle to consumer gate environmental impact data of these boxes was calculated and reported as part 1. End-of-life options of both bio- and petroleum-based boxes are an important subject which will be further studied for part 2. The energy sources in this work were taken from the Thailand energy database namely: Thai electricity grid mix (TEGM), Thai coal electricity (TCE), Thai natural gas combine cycle (TNGCC), and Thai coal integrated gasification combine cycle (TIGCC).

Methods

The materials studied were polystyrene (PS) derived from petroleum, polylactic acid (PLA) derived from corn, and PLA/cassava starch blend (PLA/starch). The tray with lid (herein after called box) was processed in a plastic manufacturing in Thailand using cast sheet extrusion and then thermoforming techniques. The functional unit is specified as 10,000 units of 8.0?×?10.0?×?2.5 cm of PS, PLA, and PLA/starch boxes which weigh 447.60, 597.60, and 549.56 kg, respectively. Three impact categories; namely global warming potential including direct greenhouse gas, and indirect land use change (LUC) emissions, acidification, and photochemical ozone formation are investigated. Finally, the normalization results including and excluding LUC consideration were compared and reported.

Results and discussion

The results from this study have shown that the total environmental impact including LUC emission of bio-based boxes were different when the various energy sources were supplied throughout the life cycle production stage. It can be seen that the PS box has lower environmental impact than PLA and PLA/starch boxes when TEGM, TCE, TNGCC, and TIGCC were used as energy supplied. LUC of renewable feedstocks, such as corn and cassava, were considered as the biggest impact of absolute scores of PLA and PLA/starch boxes. These results are consistent with Piemonte and Gironi (2010).

Conclusions

PLA and PLA/starch boxes give a slightly higher environmental impact than the PS box by 1.59 and 1.09 times, respectively, when LUC was not accounted in the absolute scores and clean energy TIGCC was used throughout the life cycle.     

Does nest box use reduce the fitness of a tree-cavity dependent mammal?

Nest boxes are frequently used in conservation programs for tree-cavity dependent wildlife. There is growing concern that the poor insulation properties of nest boxes may produce an ecological trap, because species may require microclimates less extreme or less variable than those experienced inside nest boxes. I investigated the fitness consequences of nest box use in a non-flying mammal. Fifty-two of 104 squirrel gliders (Petaurus norfolcensis) trapped over a 3-year period used nest boxes. Population modelling of the capture data revealed that the probability of apparent survival increased with increasing nest box use. There was no difference in breeding frequency between females that used or did not use nest boxes. There was no evidence that offspring development was hindered within nest boxes. These findings may arise because: (1) gliders could access tree hollows during extreme temperatures, (2) ambient temperatures were mild during the study, (3) gliders construct leaf nests which insulate against low temperatures in winter, and (4) gliders breed between autumn and spring when temperatures are relatively benign. The estimate of annual survival of animals using nest boxes (0.60), was equivalent to estimates at locations where squirrel gliders were either reliant on nest boxes (0.54) or on tree cavities (0.55) for shelter. Studies such as this need to be conducted on a range of species across a range of locations to better understand the influence of nest box use on non-flying mammals.     

Temporal variation in arthropod sampling effectiveness: the case for using the beat sheet method in cotton

Predatory insects and spiders are key elements of integrated pest management (IPM) programmes in agricultural crops such as cotton. Management decisions in IPM programmes should to be based on a reliable and efficient method for counting both predators and pests. Knowledge of the temporal constraints that influence sampling is required because arthropod abundance estimates are likely to vary over a growing season and within a day. Few studies have adequately quantified this effect using the beat sheet, a potentially important sampling method. We compared the commonly used methods of suction and visual sampling to the beat sheet, with reference to an absolute cage clamp method for determining the abundance of various arthropod taxa over 5 weeks. There were significantly more entomophagous arthropods recorded using the beat sheet and cage clamp methods than by using suction or visual sampling, and these differences were more pronounced as the plants grew. In a second trial, relative estimates of entomophagous and phytophagous arthropod abundance were made using beat sheet samples collected over a day. Beat sheet estimates of the abundance of only eight of the 43 taxa examined were found to vary significantly over a day. Beat sheet sampling is recommended in further studies of arthropod abundance in cotton, but researchers and pest management advisors should bear in mind the time of season and time of day effects.     

Control of green mold and sour rot of stored lemon by biofumigation with Muscodor albus

Control of postharvest lemon diseases by biofumigation with the volatile-producing fungus Muscodor albus was investigated. In vitro exposure to M. albus volatile compounds for 3 days killed Penicillium digitatum and Geotrichum citri-aurantii, causes of green mold and sour rot of lemons, respectively. Lemons were wound-inoculated with P. digitatum and placed in closed 11-L plastic boxes with rye grain cultures of M. albus at ambient temperature. There was no contact between the fungus and the fruit. Biofumigation for 24–72 h controlled green mold significantly, even when treatment began 24 h after inoculation. Effectiveness was related to the amount of M. albus present. In tests conducted inside a 11.7-m³ degreening room with 5 ppm ethylene at 20 °C, green mold incidence on lemons was reduced on average from 89.8 to 26.2% after exposure to M. albus for 48 h. Ethylene accelerates color development in harvested citrus fruit. M. albus had no effect on color development. Biofumigation in small boxes immediately after inoculation controlled sour rot, but was ineffective if applied 24 h later. G. citri-aurantii may be less sensitive to the volatile compounds than P. digitatum or escapes exposure within the fruit rind. Biofumigation with M. albus could control decay effectively in storage rooms or shipping packages.     

Increased microclimatic variation in artificial nests does not create ecological traps for a secondary cavity breeder,the European roller

Artificial devices are increasingly used in conservation measures to mitigate the disappearance of natural habitats. However, few studies have demonstrated their benefits for the target species, and they may pose a risk of creating ecological traps. This occurs when lower individual fitness is found in artificial habitats that are more attractive than their natural equivalents. In this study, we tested the ecological trap hypothesis on a dense population of European rollers Coracias garrulus breeding in both natural cavities and nest boxes. Our initial prediction was that the more stressful microclimatic conditions of nest boxes would lead to reduced fitness of European rollers, thus creating an ecological trap. The results showed that nest boxes were preferred over natural cavities. Despite significantly more extreme microclimatic conditions in nest boxes, we found similar breeding parameters between artificial and natural nest types. Our results also suggest that European rollers selected the nest boxes which best buffered the temperature, thus avoiding potential ecological traps. Overall our results led to the conclusion that nest boxes do not create ecological traps for European rollers in this study area. However, other species may be more sensitive to microclimatic variations or less able to avoid the least favorable nest boxes. These findings could help to inform the placement of nest boxes in order to reduce extreme temperatures and variation in humidity rates. Future studies could compare nest types for other fitness parameters, such as juvenile body condition or survival. We also recommend the ecological trap hypothesis as a useful framework to evaluate the outcomes of artificial devices used for conservation.     

The Drosophila shell game: patterning genes and morphological change

What are the mechanisms that convert cell-fate information into shape changes and movements, thus creating the biological forms that comprise tissues and organs? Tubulogenesis of the Drosophila dorsal eggshell structures provides an excellent system for studying the link between patterning and morphogenesis. Elegant genetic and molecular analyses from over a decade provide a strong foundation for understanding the combinatorial signaling events that specify dorsal anterior cell fates within the follicular epithelium overlying the oocyte. Recent studies reveal the morphogenetic events that alter that flat epithelial sheet into two tubes; these tubes form the mold for synthesizing the dorsal appendages--eggshell structures that facilitate respiration in the developing embryo. This review summarizes the mutant analyses that give insight into these patterning and morphogenetic processes.     

Nest box contentions: Are nest boxes used by the species they target?

Nest boxes have grown in popularity as a habitat management tool in Australia during the last decade. This management use remains contentious because some studies suggest nest boxes are ineffective. There are three recent contentions: (i) nest boxes mostly benefit common species, (ii) exotic species may be dominant users of nest boxes, and (iii) species of conservation concern use nest boxes infrequently. We address these contentions using data from 1865 nest boxes involving eight nest box designs. These nest boxes were installed predominantly <200 m from a road in association with highway duplication and re‐alignment across 16 projects in New South Wales. The Common Brushtail Possum (Trichosurus vulpecula) is the species of most relevance to contention 1. It used 9% of boxes overall including 26% of ‘possum’ designated boxes. The most frequent nest box users were small petaurid gliders (mostly Sugar Gliders, Petaurus breviceps) which used 63% of ‘small glider’ designated boxes. This nest box and another suited to the Sugar Glider comprised 40% of all boxes installed, so it is not surprising that this species might be a common user. Exotic species were uncommon users of the nest boxes enabling contention 2 to be rejected. Active hives of Feral Honeybees (Apis mellifera) occupied just 1% of boxes, and another 1% of boxes were used by introduced rodents and birds. The Squirrel Glider (Petaurus norfolcensis) is the species most relevant to contention 3. It was seen in 80 boxes across 11 projects, representing 7% of the three types most frequently used. These observations are not consistent with the third contention. Nest boxes can provide many important insights about the requirements and interactions of hollow‐dependent fauna. However, they are not intended as an alternative to retaining hollow‐bearing trees.     

Nest boxes in planted and regrowth Forest Red‐gum (Eucalyptus tereticornis Sm.) ecosystems

Nest boxes were deployed in planted and regrowth areas in association with a revegetation project to restore Forest Red‐gum (Eucalyptus tereticornis) ecosystems on abandoned former agricultural land. A year after revegetation began, 36 boxes were installed in each of the planted and regrowth areas in 2003, and these were monitored to 2013. Sixteen vertebrate species utilised boxes, which included breeding by four species and two species that were not detected by other survey methods. More boxes were used by fauna in the planting compared to regrowth in all but one audit. Significantly, more boxes were used by reptiles in regrowth than planting, but significantly more by birds in planting than regrowth. Nearly 90 per cent of boxes remained intact over the 10‐year period. While the study's capacity to attribute results to habitat types was limited, the results do add weight to the possibility that nest boxes made of good quality materials can provide valuable habitat for a wide range of species during the early recovery phase of reforestation projects.